MolNFT v1 · #151827 · protein
Structure of mcrbc without DNA binding domains (class 4)
6HZ8 · 5-methylcytosine-specific restriction enzyme B: “Structure of mcrbc without DNA binding domains (class 4)”. Electron microscopy, 3 ligands (GNP, GDP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #151827 on GenesisL1: 3D…
- PDB
- 6HZ8
- Type
- protein
- Length
- 4,120 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methylcytosine-specific restriction enzyme B; Protein mcrc
- EC
- 3.1.21.-
- UniProt
- P15005, P15006
- Ligands
- GNP, GDP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, G, H, I | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 290 | 48% helix, 13% strand | P15005 |
| D, J | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 284 | 42% helix, 12% strand | P15005 |
| E, F, K, L | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 285 | 45% helix, 14% strand | P15005 |
| M, N | Protein mcrc | protein | 336 | 40% helix, 20% strand | P15006 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, D, G, H, I, J
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains D, E, F, A, J, K, L, G
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.88 | 0.90 | 125 | empty |
| 2 | 1200 | 0.87 | 0.88 | 120 | empty |
| 3 | 1097 | 0.86 | 0.87 | 130 | empty |
| 4 | 847 | 0.85 | 0.88 | 92 | GDP |
| 5 | 976 | 0.85 | 0.86 | 114 | empty |
Interfaces
29 interfaces between chains.
- A–B · 2209 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 2204 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2180 Ų buried · 21 hydrogen bonds · protein-protein
- H–I · 2135 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 1949 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6HZ8 · Structure of McrBC without DNA binding domains (Class 4) · the same entry in another collection · chain N against N, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P15005
- Every structure of UniProt P15006
- Elsewhere: RCSB PDB 6HZ8 · PDBe 6HZ8 · UniProt P15005 · UniProt P15006
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